MOgene ::Pathway Analysis::

Custom Analysis

Pathway Example

Experiment: Sample A vs. Sample B are hybridized on four arrays. Average Log Ratios are calculated to indicate which genes are differentially expressed between the two samples. We determine which pathways are significantly changed in the experiment, based on the (relative) expression levels of the genes involved in the pathway.

Pathway Description	K_S	p_value	TotalGene	UpGene	DownGene
Glycolysis / Gluconeogenesis	0.29677	0.001243	42	7	3
Citrate cycle (TCA cycle)	0.4892	2.08E-05	24	4	0
Pentose phosphate pathway	0.26687	0.08738	22	3	1
Inositol metabolism	0.69206	0.293565	2	1	0
Pentose and glucuronate interconversions	0.25419	0.606319	9	0	0
Oxidative phosphorylation	0.47815	5.60E-21	104	32	4
Valine, leucine and isoleucine degradation	0.37328	6.77E-05	37	7	1
Fructose and mannose metabolism	0.12988	0.449268	44	3	4

pathwayDescription: the name of the pathway

K_S: Komolgorov-Smirnov statistics for testing if two samples comes from the same underlying distribution

p-value: that the probability that the ____expression levels of genes in a pathway can be observed soly due to randomness; it is calculated from the K_S statistics
TotalGenes : the number of genes in each pathway.

UpGenes: the number of up-regulated genes in the passway

DownGenes: the number of down-regulated genes in the passway

Note: In counting the number of up- and down- genes in the last two columns, we use the cut-offs (somewhat arbitrary) of p-value of 0.05 and fold-change of 1.3.

Pathway information is collected from KEGG website.

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